Cadmium in PDB 5azg: Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide

The structure of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide, PDB code: 5azg was solved by Y.Watanabe, Y.Fujioka, N.N.Noda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.75 / 1.81
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	63.684, 80.116, 111.500, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide (pdb code 5azg). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 14 binding sites of Cadmium where determined in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide, PDB code: 5azg:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:37.5 occ:1.00 NE2 A:HIS0 2.3 36.6 1.0 O A:GLY116 2.5 42.6 1.0 OXT A:GLY116 2.5 40.1 1.0 C A:GLY116 2.9 42.5 1.0 CE1 A:HIS0 3.2 36.9 1.0 CD2 A:HIS0 3.3 37.1 1.0 ND1 A:HIS0 4.4 36.0 1.0 CA A:GLY116 4.4 43.7 1.0 CG A:HIS0 4.4 35.8 1.0 O A:HOH317 4.8 37.7 1.0

Cadmium binding site 2 out of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:70.4 occ:1.00 OE2 A:GLU17 2.5 45.3 1.0 OE1 A:GLU17 2.8 47.5 1.0 CD A:GLU17 3.0 44.2 1.0 O C:HOH404 3.8 42.9 1.0 NZ A:LYS48 4.3 45.8 1.0 CG A:GLU17 4.5 41.0 1.0 O C:HOH405 4.5 63.3 1.0 CE1 C:PHE358 4.6 41.9 1.0 OD1 C:ASP357 5.0 57.9 1.0

Cadmium binding site 3 out of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:51.1 occ:1.00 O A:HOH301 1.7 34.7 1.0 OD1 A:ASP45 2.4 50.8 1.0 OD2 A:ASP45 2.6 49.4 1.0 CG A:ASP45 2.8 49.9 1.0 CB A:ASP45 4.3 48.0 1.0 O A:ASP45 4.4 47.2 1.0 NZ A:LYS46 4.9 56.2 1.0 CE A:LYS46 4.9 54.6 1.0 C A:ASP45 4.9 46.3 1.0 CA A:ASP45 5.0 47.2 1.0

Cadmium binding site 4 out of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:37.6 occ:1.00 O A:HOH328 2.2 47.1 1.0 OD2 A:ASP97 2.3 31.1 1.0 OD1 A:ASP97 2.7 32.5 1.0 CG A:ASP97 2.8 31.6 1.0 OE1 A:GLN96 3.9 37.8 1.0 CB A:ASP97 4.3 29.9 1.0 O A:HOH310 4.6 34.9 1.0 O A:HOH336 4.7 46.6 1.0 O A:GLN93 4.9 28.5 1.0

Cadmium binding site 5 out of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:40.5 occ:1.00 O A:HOH336 2.1 46.6 1.0 O A:HOH338 2.2 73.8 1.0 O A:HOH341 2.4 39.5 1.0 NE2 A:HIS98 2.4 30.6 1.0 O A:HOH310 2.4 34.9 1.0 O A:HOH339 2.7 48.4 1.0 CD2 A:HIS98 3.3 30.3 1.0 CE1 A:HIS98 3.4 31.8 1.0 OD2 A:ASP97 4.1 31.1 1.0 O A:HOH313 4.2 50.5 1.0 CB A:ASP97 4.5 29.9 1.0 CG A:HIS98 4.5 29.0 1.0 ND1 A:HIS98 4.5 31.0 1.0 CG A:ASP97 4.8 31.6 1.0

Cadmium binding site 6 out of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:39.0 occ:1.00 O B:HOH335 2.0 43.3 1.0 O B:HOH327 2.2 45.0 1.0 OD2 A:ASP27 2.3 38.5 1.0 OD1 B:ASP54 2.3 35.1 1.0 OD2 B:ASP54 2.4 39.8 1.0 OD1 A:ASP27 2.4 37.1 1.0 O B:HOH344 2.4 45.5 1.0 CG A:ASP27 2.6 37.4 1.0 CG B:ASP54 2.7 36.9 1.0 CB A:ASP27 4.2 36.0 1.0 CB B:ASP54 4.2 36.5 1.0 O B:HOH336 4.2 40.1 1.0 O B:HOH337 4.3 43.5 1.0 CB B:PRO52 4.6 29.4 1.0 CA A:ASP27 5.0 34.0 1.0 N B:ASP54 5.0 34.6 1.0 N A:ASP27 5.0 34.3 1.0 CA B:ASP54 5.0 35.0 1.0

Cadmium binding site 7 out of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:51.9 occ:1.00 O A:HOH303 2.4 39.8 1.0 O B:HOH337 2.5 43.5 1.0 OD1 A:ASP27 4.0 37.1 1.0 O B:HOH335 4.2 43.3 1.0 OD2 B:ASP27 4.3 40.8 1.0 O B:HOH344 4.4 45.5 1.0 O B:HOH343 4.7 50.2 1.0 OG A:SER53 4.7 30.9 1.0

Cadmium binding site 8 out of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:42.1 occ:1.00 O B:HOH331 2.0 52.7 1.0 OD2 B:ASP27 2.1 40.8 1.0 OD2 A:ASP54 2.4 34.7 1.0 O B:HOH343 2.4 50.2 1.0 OD1 A:ASP54 2.6 37.5 1.0 CG A:ASP54 2.8 34.7 1.0 CG B:ASP27 2.9 36.6 1.0 OD1 B:ASP27 2.9 38.4 1.0 CB B:ASP27 4.3 34.6 1.0 CB A:ASP54 4.3 33.4 1.0 O A:HOH303 4.3 39.8 1.0 OG A:SER53 4.4 30.9 1.0 O B:HOH337 4.6 43.5 1.0 NE B:ARG28 4.7 30.9 1.0

Cadmium binding site 9 out of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd201 b:33.7 occ:1.00 O B:HOH313 2.2 63.4 1.0 NE2 B:HIS0 2.2 30.8 1.0 O B:GLY116 2.3 53.9 1.0 OXT B:GLY116 2.5 48.4 1.0 C B:GLY116 2.8 50.9 1.0 O B:HOH304 3.1 41.1 1.0 CE1 B:HIS0 3.2 31.0 1.0 CD2 B:HIS0 3.2 31.9 1.0 CA B:GLY116 4.3 49.8 1.0 ND1 B:HIS0 4.3 30.5 1.0 CG B:HIS0 4.4 31.5 1.0

Cadmium binding site 10 out of 14 in the Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Lgg-1 Complexed with A Unc-51 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd202 b:33.3 occ:1.00 O B:HOH340 2.2 41.0 1.0 NE2 B:HIS99 2.3 28.0 1.0 O B:HOH347 2.6 39.8 1.0 CE1 B:HIS99 3.2 29.6 1.0 CD2 B:HIS99 3.5 28.6 1.0 O B:HOH314 4.3 40.5 1.0 ND1 B:HIS99 4.4 29.2 1.0 CG B:HIS99 4.5 28.3 1.0 O B:HOH315 5.0 49.6 1.0

F.Wu, Y.Watanabe, X.Y.Guo, X.Qi, P.Wang, H.Y.Zhao, Z.Wang, Y.Fujioka, H.Zhang, J.Q.Ren, T.C.Fang, Y.X.Shen, W.Feng, J.J.Hu, N.N.Noda, H.Zhang. Structural Basis of the Differential Function of the Two C. Elegans ATG8 Homologs, Lgg-1 and Lgg-2, in Autophagy Mol.Cell V. 60 914 2015.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2015.11.019